What is going on with the Extrusion?
By default your extrusion will follow the normal of your face, so if your face is slightly tilted on the Z axis it won't follow the Y axis. If you want your extrusion to follow the Y axis, you need to constraint the extrusion: press E to extrude, then Y. Also don't forget to activate the Clipping option of the Mirror modifier, it will prevent the creation of any inner faces.